rs772941507
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001244710.2(GFPT1):c.1041A>T(p.Ile347=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,607,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
GFPT1
NM_001244710.2 synonymous
NM_001244710.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.834
Genes affected
GFPT1 (HGNC:4241): (glutamine--fructose-6-phosphate transaminase 1) This gene encodes the first and rate-limiting enzyme of the hexosamine pathway and controls the flux of glucose into the hexosamine pathway. The product of this gene catalyzes the formation of glucosamine 6-phosphate. [provided by RefSeq, Sep 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
Variant 2-69345968-T-A is Benign according to our data. Variant chr2-69345968-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 473140.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.834 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GFPT1 | NM_001244710.2 | c.1041A>T | p.Ile347= | synonymous_variant | 12/20 | ENST00000357308.9 | |
GFPT1 | NM_002056.4 | c.987A>T | p.Ile329= | synonymous_variant | 11/19 | ||
GFPT1 | XM_017003801.2 | c.1116A>T | p.Ile372= | synonymous_variant | 12/20 | ||
GFPT1 | XM_017003802.3 | c.1062A>T | p.Ile354= | synonymous_variant | 11/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GFPT1 | ENST00000357308.9 | c.1041A>T | p.Ile347= | synonymous_variant | 12/20 | 5 | NM_001244710.2 | ||
GFPT1 | ENST00000361060.5 | c.987A>T | p.Ile329= | synonymous_variant | 11/19 | 1 | P1 | ||
GFPT1 | ENST00000674507.1 | c.987A>T | p.Ile329= | synonymous_variant | 11/18 | ||||
GFPT1 | ENST00000674438.1 | c.771A>T | p.Ile257= | synonymous_variant | 9/17 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152258Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251136Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135746
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GnomAD4 exome AF: 0.000142 AC: 206AN: 1454904Hom.: 0 Cov.: 28 AF XY: 0.000135 AC XY: 98AN XY: 724302
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74382
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital myasthenic syndrome 12 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at